[English] 日本語
Yorodumi
- PDB-5cdo: 3.15A structure of QPT-1 with S.aureus DNA gyrase and DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5cdo
Title3.15A structure of QPT-1 with S.aureus DNA gyrase and DNA
Components
  • (DNA gyrase subunit ...) x 2
  • DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
KeywordsISOMERASE / TYPE IIA TOPOISOMERASE / ANTIBACTERIAL / INHIBITOR
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / response to antibiotic / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Rossmann fold - #670 / DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / : / DNA gyrase C-terminal domain, beta-propeller / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal ...Rossmann fold - #670 / DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / : / DNA gyrase C-terminal domain, beta-propeller / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / Toprim domain / DNA topoisomerase, type IIA-like domain superfamily / Toprim domain profile. / TOPRIM domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-50M / Chem-53L / Chem-53M / : / DNA / DNA (> 10) / DNA gyrase subunit B / DNA gyrase subunit A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.15 Å
AuthorsBax, B.D. / Srikannathasan, V. / Chan, P.F.
Citation
Journal: Nat Commun / Year: 2015
Title: Structural basis of DNA gyrase inhibition by antibacterial QPT-1, anticancer drug etoposide and moxifloxacin.
Authors: Chan, P.F. / Srikannathasan, V. / Huang, J. / Cui, H. / Fosberry, A.P. / Gu, M. / Hann, M.M. / Hibbs, M. / Homes, P. / Ingraham, K. / Pizzollo, J. / Shen, C. / Shillings, A.J. / Spitzfaden, ...Authors: Chan, P.F. / Srikannathasan, V. / Huang, J. / Cui, H. / Fosberry, A.P. / Gu, M. / Hann, M.M. / Hibbs, M. / Homes, P. / Ingraham, K. / Pizzollo, J. / Shen, C. / Shillings, A.J. / Spitzfaden, C.E. / Tanner, R. / Theobald, A.J. / Stavenger, R.A. / Bax, B.D. / Gwynn, M.N.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Crystallization and initial crystallographic analysis of covalent DNA-cleavage complexes of Staphyloccocus aureus DNA gyrase with QPT-1, moxifloxacin and etoposide.
Authors: Srikannathasan, V. / Wohlkonig, A. / Shillings, A. / Singh, O. / Chan, P.F. / Huang, J. / Gwynn, M.N. / Fosberry, A.P. / Homes, P. / Hibbs, M. / Theobald, A.J. / Spitzfaden, C. / Bax, B.D.
History
DepositionJul 4, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA gyrase subunit A
B: DNA gyrase subunit B,DNA gyrase subunit B
C: DNA gyrase subunit A
D: DNA gyrase subunit B,DNA gyrase subunit B
E: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
F: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
R: DNA gyrase subunit A
S: DNA gyrase subunit B,DNA gyrase subunit B
T: DNA gyrase subunit A
U: DNA gyrase subunit B,DNA gyrase subunit B
V: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
W: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)330,73833
Polymers328,15712
Non-polymers2,58121
Water1,47782
1
A: DNA gyrase subunit A
B: DNA gyrase subunit B,DNA gyrase subunit B
C: DNA gyrase subunit A
D: DNA gyrase subunit B,DNA gyrase subunit B
E: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
F: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,37917
Polymers164,0796
Non-polymers1,30011
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
R: DNA gyrase subunit A
S: DNA gyrase subunit B,DNA gyrase subunit B
T: DNA gyrase subunit A
U: DNA gyrase subunit B,DNA gyrase subunit B
V: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
W: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,36016
Polymers164,0796
Non-polymers1,28110
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.472, 170.211, 124.579
Angle α, β, γ (deg.)90.000, 102.750, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
DNA gyrase subunit ... , 2 types, 8 molecules ACRTBDSU

#1: Protein
DNA gyrase subunit A


Mass: 54777.379 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain N315) (bacteria)
Strain: N315 / Gene: gyrA, SA0006 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99XG5, EC: 5.99.1.3
#2: Protein
DNA gyrase subunit B,DNA gyrase subunit B


Mass: 21111.018 Da / Num. of mol.: 4 / Fragment: residues 417-638,residues 417-638
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain N315) (bacteria)
Strain: N315 / Gene: gyrB, SA0005 / Production host: Escherichia coli (E. coli) / References: UniProt: P66937, EC: 5.99.1.3

-
DNA chain , 1 types, 4 molecules EFVW

#3: DNA chain
DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')


Mass: 6150.966 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

-
Non-polymers , 8 types, 103 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Source: (synth.) synthetic construct (others)
#8: Chemical ChemComp-53M / (2R,4S,4aS)-4',6'-dihydroxy-2,4-dimethyl-8-nitro-1,2,4,4a-tetrahydro-2'H,6H-spiro[1,4-oxazino[4,3-a]quinoline-5,5'-pyrimidin]-2'-one


Mass: 374.348 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H18N4O6
#9: Chemical ChemComp-53L / (2R,4S,4aS,5S)-6'-hydroxy-2,4-dimethyl-8-nitro-1,2,4,4a-tetrahydro-2'H,6H-spiro[1,4-oxazino[4,3-a]quinoline-5,5'-pyrimidine]-2',4'(3'H)-dione


Mass: 374.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18N4O6
#10: Chemical ChemComp-50M / (2R,4S,4aS,5R)-6'-hydroxy-2,4-dimethyl-8-nitro-1,2,4,4a-tetrahydro-2'H,6H-spiro[1,4-oxazino[4,3-a]quinoline-5,5'-pyrimidine]-2',4'(3'H)-dione


Mass: 374.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18N4O6
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.86 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.2 / Details: 150mM BisTris pH6.2, 11% PEG 5000 MME / PH range: 6.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97627 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97627 Å / Relative weight: 1
ReflectionResolution: 3.15→58.42 Å / Num. obs: 62354 / % possible obs: 98.2 % / Redundancy: 3 % / Biso Wilson estimate: 48.78 Å2 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.087 / Net I/σ(I): 7.7 / Num. measured all: 185026
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
3.15-3.2630.4142.81847261750.28698.7
12.2-58.422.90.06215.4315410780.04394.9

-
Processing

Software
NameVersionClassification
Aimless3.3.16data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHENIXphasing
RefinementResolution: 3.15→58.415 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2465 2510 4.03 %
Rwork0.2151 59797 -
obs0.2163 62307 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 176.38 Å2 / Biso mean: 50.3513 Å2 / Biso min: 8.99 Å2
Refinement stepCycle: final / Resolution: 3.15→58.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20865 1597 274 82 22818
Biso mean--31.29 30.75 -
Num. residues----2751
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00523130
X-RAY DIFFRACTIONf_angle_d0.97231595
X-RAY DIFFRACTIONf_chiral_restr0.0633581
X-RAY DIFFRACTIONf_plane_restr0.0043893
X-RAY DIFFRACTIONf_dihedral_angle_d18.068858
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.15-3.21060.33511360.29623362349899
3.2106-3.27610.34761340.2823305343998
3.2761-3.34730.30061320.26293335346798
3.3473-3.42520.27131470.25943303345098
3.4252-3.51080.30141470.24713293344097
3.5108-3.60580.24571380.22573336347499
3.6058-3.71180.29891400.22583331347198
3.7118-3.83160.21961410.21623343348499
3.8316-3.96850.24991330.21243303343698
3.9685-4.12740.25741370.19743355349299
4.1274-4.31520.21191490.19263297344698
4.3152-4.54260.23161430.18353291343497
4.5426-4.82710.21811450.183315346098
4.8271-5.19960.21091300.18893354348498
5.1996-5.72240.23311420.20613331347398
5.7224-6.54950.24141260.21733310343697
6.5495-8.2480.24631520.213307345997
8.248-58.42530.20371380.20583326346496
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5636-0.07680.01040.56710.05150.34010.0032-0.00250.1484-0.12170.00990.15020.046-0.0904-0.01730.2234-0.0389-0.02860.2799-0.01580.366435.4346-30.669755.1404
21.7507-0.23330.37991.0349-0.21682.10350.3601-0.3944-0.46940.6147-0.1512-0.28130.53980.2838-0.16240.4766-0.0122-0.11510.52340.1030.396641.3698-50.775983.7504
31.9179-0.0493-0.1412.41520.0861.9929-0.23330.1537-0.423-0.5620.0649-0.10210.5494-0.29510.13270.5267-0.17630.03090.4177-0.00730.369727.9003-52.487133.5457
42.49090.9289-0.01742.21110.24951.2493-0.05060.05410.1390.12570.21320.259-0.0804-0.0019-0.10670.30020.0312-0.020.3068-0.03020.479945.620916.951562.6068
52.3140.02841.13541.40810.47012.3393-0.0796-0.5023-0.21340.25010.23520.54660.0393-0.6717-0.17270.2209-0.15180.02390.56160.04540.495922.5972-42.427880.6624
60.61910.0835-0.13022.8320.3491.14230.0458-0.02340.2137-0.1856-0.0715-0.2085-0.2662-0.03430.02330.18580.0707-0.0110.2138-0.03530.388377.9338-27.152968.725
71.35250.00870.42481.29410.05030.93660.11710.3717-0.2038-0.581-0.04690.3105-0.1134-0.3065-0.07640.59170.1399-0.05350.52-0.02030.329962.8217-52.367338.1463
82.2358-0.99680.38161.9638-0.90481.77660.00660.19810.25-0.1853-0.0836-0.2836-0.21380.0755-0.04260.3349-0.05880.06770.2167-0.02470.356366.258416.777359.5224
91.9228-0.10580.26242.0527-0.27092.4983-0.1189-0.0798-0.52250.22190.10840.16420.48950.13260.03480.35780.10350.03910.42950.03270.365775.5725-55.424288.6761
102.5805-0.1259-0.81773.92620.18752.0048-0.12030.39060.0647-0.55360.2171-0.57220.02750.1477-0.05130.53710.09160.09260.4323-0.0170.464682.8628-46.82441.6012
111.9227-0.5671-0.24970.36030.08240.48150.04310.17280.3405-0.0465-0.0207-0.0748-0.18760.113-0.03440.2367-0.0630.00850.24060.03420.322487.151-28.0829-5.6642
121.2247-0.18130.29131.04790.2391.52570.2434-0.37280.59570.5413-0.11440.4912-0.466-0.22010.00360.72-0.03690.20390.4437-0.11350.492579.6406-7.3421.6146
132.89090.9014-0.1651.7516-0.20670.7951-0.0831-0.0235-0.3636-0.16390.07660.07170.0551-0.02620.10340.4052-0.0090.07260.26480.07360.582275.7093-76.00432.9549
141.14530.3305-0.28092.5536-0.83441.38150.05440.61111.0659-1.0647-0.2836-0.5391-0.7066-0.00310.22790.6366-0.3-0.04420.72380.52621.082195.7767-7.7664-28.0962
151.6378-0.26380.11591.45880.02522.51160.0822-0.82660.74280.8148-0.0704-0.2159-0.04890.7657-0.08520.5098-0.2874-0.01870.6935-0.19110.597999.108-14.535218.9504
161.26820.36440.4352.7138-0.35921.08810.0138-0.1012-0.0704-0.167-0.02060.01660.0714-0.03290.01280.27610.03350.11480.19310.01950.256543.6971-31.34137.9993
171.69370.0619-0.54050.8369-0.28711.4376-0.00220.43980.0792-0.4734-0.1098-0.43420.06980.20310.1130.67140.06490.18490.44380.08290.452757.282-7.1783-24.2176
181.7458-0.4071-0.34791.24330.10211.289-0.15030.1339-0.1863-0.14370.1383-0.0670.05820.0169-0.01370.3959-0.04150.07660.22210.04110.409155.5728-75.0636-0.5172
191.18070.56560.05071.75440.96971.92470.0565-0.34470.54521.0912-0.24180.1818-0.5640.06960.26390.78390.02450.01560.5076-0.18090.488846.7087-2.857427.0304
201.964-0.0678-0.98580.9750.62621.71550.00120.6570.3141-0.9435-0.11960.16210.1799-0.3054-0.12790.57330.0259-0.01260.43240.12680.458637.8421-12.1789-19.4359
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1((chain A and (resid 28:244 or resid 328:369 or resid 451:490)) or (chain E) or (chain F))A28 - 244
2X-RAY DIFFRACTION1((chain A and (resid 28:244 or resid 328:369 or resid 451:490)) or (chain E) or (chain F))A328 - 369
3X-RAY DIFFRACTION1((chain A and (resid 28:244 or resid 328:369 or resid 451:490)) or (chain E) or (chain F))A451 - 490
4X-RAY DIFFRACTION2((chain B and (resid 417:608)))B0
5X-RAY DIFFRACTION3((chain A and (resid 245:327)))A0
6X-RAY DIFFRACTION4((chain A and (resid 370:450)))A0
7X-RAY DIFFRACTION5((chain A and (resid 10:27)) or (chain B and (resid 609:638)))A0
8X-RAY DIFFRACTION6((chain C and (resid 28:244 or resid 328:369 or resid 451:491)))C28 - 244
9X-RAY DIFFRACTION6((chain C and (resid 28:244 or resid 328:369 or resid 451:491)))C328 - 369
10X-RAY DIFFRACTION6((chain C and (resid 28:244 or resid 328:369 or resid 451:491)))C451 - 491
11X-RAY DIFFRACTION7((chain D and (resid 417:608)))D0
12X-RAY DIFFRACTION8((chain C and (resid 375:450)))C0
13X-RAY DIFFRACTION9((chain C and (resid 245:327)))C0
14X-RAY DIFFRACTION10((chain C and (resid 10:27)) or (chain D and (resid 609:637)))C0
15X-RAY DIFFRACTION11((chain R and (resid 28:244 or resid 328:369 or resid 451:490)) or (chain V) or (chain W))R28 - 244
16X-RAY DIFFRACTION11((chain R and (resid 28:244 or resid 328:369 or resid 451:490)) or (chain V) or (chain W))R328 - 369
17X-RAY DIFFRACTION11((chain R and (resid 28:244 or resid 328:369 or resid 451:490)) or (chain V) or (chain W))R451 - 490
18X-RAY DIFFRACTION12((chain S and (resid 417:608)))S0
19X-RAY DIFFRACTION13((chain R and (resid 375:450)))R0
20X-RAY DIFFRACTION14((chain R and (resid 245:327)))R0
21X-RAY DIFFRACTION15((chain R and (resid 11:27)) or (chain S and (resid 609:637)))R0
22X-RAY DIFFRACTION16((chain T and (resid 28:244 or resid 328:369 or resid 451:490)))T28 - 244
23X-RAY DIFFRACTION16((chain T and (resid 28:244 or resid 328:369 or resid 451:490)))T328 - 369
24X-RAY DIFFRACTION16((chain T and (resid 28:244 or resid 328:369 or resid 451:490)))T451 - 490
25X-RAY DIFFRACTION17((chain U and (resid 417:608)))U0
26X-RAY DIFFRACTION18((chain T and (resid 375:450)))T0
27X-RAY DIFFRACTION19((chain T and (resid 245:327)))T0
28X-RAY DIFFRACTION20((chain T and (resid 10:27)) or (chain U and (resid 609:637)))T0

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more